Only displaying parameters that differ from the pipeline defaults.
{"runName":"marvelous_hugle","containerEngine":"apptainer","launchDir":"/powerplant/workspace/hrasrb/Repo/assembly_qc","workDir":"/powerplant/workspace/hrasrb/Repo/assembly_qc/work","projectDir":"/powerplant/workspace/hrasrb/Repo/assembly_qc","userName":"hrasrb","profile":"pfr,apptainer","input":"/powerplant/workspace/hrasrb/Repo/assembly_qc/pfr/assemblysheet_hrasrb.csv","outdir":"./cleaned_blueberry_haplotype_results","ncbi_fcs_adaptor_empire":"euk","ncbi_fcs_gx_tax_id":"3750","ncbi_fcs_gx_db_path":"/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24","busco_skip":"false","busco_mode":"geno","busco_lineage_datasets":"embryophyta_odb10 eudicots_odb10","busco_download_path":"/workspace/ComparativeDataSources/BUSCO/assemblyqc","tidk_skip":"false","tidk_repeat_seq":"TTTAGGG","lai_skip":"false","kraken2_db_path":"/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314","synteny_xref_assemblies":"/workspace/assemblyqc/testdata/default/xrefsheet.csv","config_profile_name":"Plant&Food profile","config_profile_description":"Plant&Food profile using SLURM in combination with Apptainer"}
Pipeline Tools
Following is a non-exhaustive list of tools used to generate this report.
Contig-related stats are based on the assumption that the assemblathon_stats_n_limit (100) parameter is specified correctly. If you
are not certain of the value of the n_limit parameter, please ignore the contig-related stats.
M7_hap1_clean
Stat
Value
Assembly
classified_M7_plus_unclassified_hap1.clean.fa
Number of scaffolds
412
Total size of scaffolds
531169080
Longest scaffold
14681403
Shortest scaffold
15542
Number of scaffolds > 1K nt
412
Percentage of scaffolds > 1K nt
100.0
Number of scaffolds > 10K nt
412
Percentage of scaffolds > 10K nt
100.0
Number of scaffolds > 100K nt
259
Percentage of scaffolds > 100K nt
62.9
Number of scaffolds > 1M nt
121
Percentage of scaffolds > 1M nt
29.4
Number of scaffolds > 10M nt
6
Percentage of scaffolds > 10M nt
1.5
Mean scaffold size
1289245
Median scaffold size
245799
N50 scaffold length
5202741
L50 scaffold count
34
scaffold %A
30.74
scaffold %C
19.27
scaffold %G
19.27
scaffold %T
30.72
scaffold %N
0.0
scaffold %non-ACGTN
0.0
Number of scaffold non-ACGTN nt
0
Percentage of assembly in scaffolded contigs
0.0
Percentage of assembly in unscaffolded contigs
100.0
Average number of contigs per scaffold
1.0
Mean length of breaks (>=100Ns) between contigs in scaffold
0
Number of contigs
412
Number of contigs in scaffolds
0
Number of contigs not in scaffolds
412
Total size of contigs
531169080
Longest contig
14681403
Shortest contig
15542
Number of contigs > 1K nt
412
Percentage of contigs > 1K nt
100.0
Number of contigs > 10K nt
412
Percentage of contigs > 10K nt
100.0
Number of contigs > 100K nt
259
Percentage of contigs > 100K nt
62.9
Number of contigs > 1M nt
121
Percentage of contigs > 1M nt
29.4
Number of contigs > 10M nt
6
Percentage of contigs > 10M nt
1.5
Mean contig size
1289245
Median contig size
245799
N50 contig length
5202741
L50 contig count
34
contig %A
30.74
contig %C
19.27
contig %G
19.27
contig %T
30.72
contig %N
0.0
contig %non-ACGTN
0.0
Number of contig non-ACGTN nt
0
M7_hap2_clean
Stat
Value
Assembly
classified_M7_plus_unclassified_hap2.clean.fa
Number of scaffolds
378
Total size of scaffolds
522235882
Longest scaffold
17018523
Shortest scaffold
16806
Number of scaffolds > 1K nt
378
Percentage of scaffolds > 1K nt
100.0
Number of scaffolds > 10K nt
378
Percentage of scaffolds > 10K nt
100.0
Number of scaffolds > 100K nt
263
Percentage of scaffolds > 100K nt
69.6
Number of scaffolds > 1M nt
117
Percentage of scaffolds > 1M nt
31.0
Number of scaffolds > 10M nt
8
Percentage of scaffolds > 10M nt
2.1
Mean scaffold size
1381576
Median scaffold size
297909
N50 scaffold length
5120845
L50 scaffold count
31
scaffold %A
30.73
scaffold %C
19.29
scaffold %G
19.28
scaffold %T
30.69
scaffold %N
0.0
scaffold %non-ACGTN
0.0
Number of scaffold non-ACGTN nt
0
Percentage of assembly in scaffolded contigs
0.0
Percentage of assembly in unscaffolded contigs
100.0
Average number of contigs per scaffold
1.0
Mean length of breaks (>=100Ns) between contigs in scaffold
0
Number of contigs
378
Number of contigs in scaffolds
0
Number of contigs not in scaffolds
378
Total size of contigs
522235882
Longest contig
17018523
Shortest contig
16806
Number of contigs > 1K nt
378
Percentage of contigs > 1K nt
100.0
Number of contigs > 10K nt
378
Percentage of contigs > 10K nt
100.0
Number of contigs > 100K nt
263
Percentage of contigs > 100K nt
69.6
Number of contigs > 1M nt
117
Percentage of contigs > 1M nt
31.0
Number of contigs > 10M nt
8
Percentage of contigs > 10M nt
2.1
Mean contig size
1381576
Median contig size
297909
N50 contig length
5120845
L50 contig count
31
contig %A
30.73
contig %C
19.29
contig %G
19.28
contig %T
30.69
contig %N
0.0
contig %non-ACGTN
0.0
Number of contig non-ACGTN nt
0
Nui_hap1_clean
Stat
Value
Assembly
classified_Nui_plus_unclassified_hap1.clean.fa
Number of scaffolds
774
Total size of scaffolds
522862822
Longest scaffold
19924815
Shortest scaffold
12307
Number of scaffolds > 1K nt
774
Percentage of scaffolds > 1K nt
100.0
Number of scaffolds > 10K nt
774
Percentage of scaffolds > 10K nt
100.0
Number of scaffolds > 100K nt
341
Percentage of scaffolds > 100K nt
44.1
Number of scaffolds > 1M nt
114
Percentage of scaffolds > 1M nt
14.7
Number of scaffolds > 10M nt
6
Percentage of scaffolds > 10M nt
0.8
Mean scaffold size
675533
Median scaffold size
72322
N50 scaffold length
4551404
L50 scaffold count
34
scaffold %A
30.79
scaffold %C
19.21
scaffold %G
19.22
scaffold %T
30.78
scaffold %N
0.0
scaffold %non-ACGTN
0.0
Number of scaffold non-ACGTN nt
0
Percentage of assembly in scaffolded contigs
0.0
Percentage of assembly in unscaffolded contigs
100.0
Average number of contigs per scaffold
1.0
Mean length of breaks (>=100Ns) between contigs in scaffold
0
Number of contigs
774
Number of contigs in scaffolds
0
Number of contigs not in scaffolds
774
Total size of contigs
522862822
Longest contig
19924815
Shortest contig
12307
Number of contigs > 1K nt
774
Percentage of contigs > 1K nt
100.0
Number of contigs > 10K nt
774
Percentage of contigs > 10K nt
100.0
Number of contigs > 100K nt
341
Percentage of contigs > 100K nt
44.1
Number of contigs > 1M nt
114
Percentage of contigs > 1M nt
14.7
Number of contigs > 10M nt
6
Percentage of contigs > 10M nt
0.8
Mean contig size
675533
Median contig size
72322
N50 contig length
4551404
L50 contig count
34
contig %A
30.79
contig %C
19.21
contig %G
19.22
contig %T
30.78
contig %N
0.0
contig %non-ACGTN
0.0
Number of contig non-ACGTN nt
0
Nui_hap2_clean
Stat
Value
Assembly
classified_Nui_plus_unclassified_hap2.clean.fa
Number of scaffolds
483
Total size of scaffolds
532617838
Longest scaffold
13744249
Shortest scaffold
15236
Number of scaffolds > 1K nt
483
Percentage of scaffolds > 1K nt
100.0
Number of scaffolds > 10K nt
483
Percentage of scaffolds > 10K nt
100.0
Number of scaffolds > 100K nt
313
Percentage of scaffolds > 100K nt
64.8
Number of scaffolds > 1M nt
134
Percentage of scaffolds > 1M nt
27.7
Number of scaffolds > 10M nt
6
Percentage of scaffolds > 10M nt
1.2
Mean scaffold size
1102728
Median scaffold size
212237
N50 scaffold length
3832205
L50 scaffold count
38
scaffold %A
30.77
scaffold %C
19.23
scaffold %G
19.23
scaffold %T
30.77
scaffold %N
0.0
scaffold %non-ACGTN
0.0
Number of scaffold non-ACGTN nt
0
Percentage of assembly in scaffolded contigs
0.0
Percentage of assembly in unscaffolded contigs
100.0
Average number of contigs per scaffold
1.0
Mean length of breaks (>=100Ns) between contigs in scaffold
0
Number of contigs
483
Number of contigs in scaffolds
0
Number of contigs not in scaffolds
483
Total size of contigs
532617838
Longest contig
13744249
Shortest contig
15236
Number of contigs > 1K nt
483
Percentage of contigs > 1K nt
100.0
Number of contigs > 10K nt
483
Percentage of contigs > 10K nt
100.0
Number of contigs > 100K nt
313
Percentage of contigs > 100K nt
64.8
Number of contigs > 1M nt
134
Percentage of contigs > 1M nt
27.7
Number of contigs > 10M nt
6
Percentage of contigs > 10M nt
1.2
Mean contig size
1102728
Median contig size
212237
N50 contig length
3832205
L50 contig count
38
contig %A
30.77
contig %C
19.23
contig %G
19.23
contig %T
30.77
contig %N
0.0
contig %non-ACGTN
0.0
Number of contig non-ACGTN nt
0
BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy
orthologs.
Reference:
Manni M., Berkeley M.R., Seppey M., Simao F.A., Zdobnov E.M. 2021. BUSCO update: novel and streamlined
workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and
viral genomes. arXiv:2106.11799 [q-bio] [Internet]. Available from:
arxiv.org/abs/2106.11799
Version: 5.6.1
Summary
Assembly
Lineage
Percentages
M7_hap1_clean
eudicots_odb10
C:95.6%[S:88.5%,D:7.1%],F:1.0%,M:3.4%,n:2326
M7_hap1_clean
embryophyta_odb10
C:96.9%[S:89.8%,D:7.1%],F:1.1%,M:2.0%,n:1614
M7_hap2_clean
embryophyta_odb10
C:96.3%[S:89.9%,D:6.4%],F:0.9%,M:2.8%,n:1614
M7_hap2_clean
eudicots_odb10
C:94.9%[S:88.2%,D:6.7%],F:1.0%,M:4.1%,n:2326
Nui_hap1_clean
eudicots_odb10
C:93.8%[S:87.4%,D:6.4%],F:1.2%,M:5.0%,n:2326
Nui_hap1_clean
embryophyta_odb10
C:95.5%[S:89.1%,D:6.4%],F:1.2%,M:3.3%,n:1614
Nui_hap2_clean
eudicots_odb10
C:94.9%[S:87.7%,D:7.2%],F:1.0%,M:4.1%,n:2326
Nui_hap2_clean
embryophyta_odb10
C:96.5%[S:89.7%,D:6.8%],F:0.9%,M:2.6%,n:1614
Results
Event
Value
Search Percentages
C:95.6%[S:88.5%,D:7.1%],F:1.0%,M:3.4%,n:2326
Event
Frequency
Complete BUSCOs (C)
2224
Complete and single-copy BUSCOs (S)
2058
Complete and duplicated BUSCOs (D)
166
Fragmented BUSCOs (F)
23
Missing BUSCOs (M)
79
Total BUSCO groups searched
2326
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:96.9%[S:89.8%,D:7.1%],F:1.1%,M:2.0%,n:1614
Event
Frequency
Complete BUSCOs (C)
1565
Complete and single-copy BUSCOs (S)
1450
Complete and duplicated BUSCOs (D)
115
Fragmented BUSCOs (F)
18
Missing BUSCOs (M)
31
Total BUSCO groups searched
1614
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:96.3%[S:89.9%,D:6.4%],F:0.9%,M:2.8%,n:1614
Event
Frequency
Complete BUSCOs (C)
1554
Complete and single-copy BUSCOs (S)
1451
Complete and duplicated BUSCOs (D)
103
Fragmented BUSCOs (F)
15
Missing BUSCOs (M)
45
Total BUSCO groups searched
1614
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:94.9%[S:88.2%,D:6.7%],F:1.0%,M:4.1%,n:2326
Event
Frequency
Complete BUSCOs (C)
2206
Complete and single-copy BUSCOs (S)
2051
Complete and duplicated BUSCOs (D)
155
Fragmented BUSCOs (F)
24
Missing BUSCOs (M)
96
Total BUSCO groups searched
2326
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:93.8%[S:87.4%,D:6.4%],F:1.2%,M:5.0%,n:2326
Event
Frequency
Complete BUSCOs (C)
2183
Complete and single-copy BUSCOs (S)
2034
Complete and duplicated BUSCOs (D)
149
Fragmented BUSCOs (F)
28
Missing BUSCOs (M)
115
Total BUSCO groups searched
2326
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:95.5%[S:89.1%,D:6.4%],F:1.2%,M:3.3%,n:1614
Event
Frequency
Complete BUSCOs (C)
1542
Complete and single-copy BUSCOs (S)
1438
Complete and duplicated BUSCOs (D)
104
Fragmented BUSCOs (F)
19
Missing BUSCOs (M)
53
Total BUSCO groups searched
1614
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:94.9%[S:87.7%,D:7.2%],F:1.0%,M:4.1%,n:2326
Event
Frequency
Complete BUSCOs (C)
2207
Complete and single-copy BUSCOs (S)
2039
Complete and duplicated BUSCOs (D)
168
Fragmented BUSCOs (F)
24
Missing BUSCOs (M)
95
Total BUSCO groups searched
2326
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
Results
Event
Value
Search Percentages
C:96.5%[S:89.7%,D:6.8%],F:0.9%,M:2.6%,n:1614
Event
Frequency
Complete BUSCOs (C)
1556
Complete and single-copy BUSCOs (S)
1447
Complete and duplicated BUSCOs (D)
109
Fragmented BUSCOs (F)
14
Missing BUSCOs (M)
44
Total BUSCO groups searched
1614
Parameters and Dependencies
Parameter
Value
Version
5.6.1
Lineage create on
2024-01-08
mode
euk_genome_met
predictor
metaeuk
Dependency
Version
hmmsearch
3.1
bbtools
39.01
metaeuk
6.a5d39d9
A toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes.